[R-sig-ME] [R] nlme formula from model specification
ONKELINX, Thierry
Thierry.ONKELINX at inbo.be
Thu Sep 2 17:04:34 CEST 2010
Dear Mikkel,
I really liked Zuur et al (2009). It requires less mathematical skills to read than Pinheiro and Bates.
@BOOK{ZuurMixedModels,
title = {Mixed Effects Models and Extensions in Ecology with R},
publisher = {Springer New York},
year = {2009},
author = {Zuur, Alain F. and Ieno, Elena N. and Walker, Neil J. and Saveliev,
Anatoly A. and Smith, Graham M.},
doi = {10.1007/978-0-387-87458-6},
owner = {thierry_onkelinx},
timestamp = {2009.11.30}
}
Best regards,
Thierry
----------------------------------------------------------------------------
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium
Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
> -----Oorspronkelijk bericht-----
> Van: Mikkel Meyer Andersen [mailto:mikl at mikl.dk]
> Verzonden: donderdag 2 september 2010 14:21
> Aan: ONKELINX, Thierry
> CC: r-help at r-project.org; r-sig-mixed-models at r-project.org
> Onderwerp: Re: [R] nlme formula from model specification
>
> Dear Thierry,
>
> Thanks for the quick answer. I'm moving this to
> r-sig-mixed-models (but also posting on r-help to notify).
>
> I reserved "Mixed-effects models in S and S-PLUS" by Pinheiro
> and Bates, New York : Springer, 2000. Do you know any other
> good references?
>
> Cheers, Mikkel.
>
> 2010/9/2 ONKELINX, Thierry <Thierry.ONKELINX at inbo.be>:
> > Dear Mikkel,
> >
> > You need to do some reading on terminology.
> >
> > In your model the fixed effects are channel 1, 2 and 3.
> samplenumber
> > is a random effect and the error term is an error term
> >
> > The model you described has the notation below. You do not need to
> > create the grouped data structure.
> >
> > lme(channel0 ~ pos + samplenumber + channel1 + channel2 + channel3,
> > random = ~ 1 | samplenumber,
> > correlation = corAR1(value = 0.5, form = ~ pos | samplenumber),
> > data = channel.matrix)
> >
> > HTH,
> >
> > Thierry
> >
> > PS There is a dedicated mailing list for mixed models:
> > R-sig-mixed-models
> >
> >
> ----------------------------------------------------------------------
> > --
> > ----
> > ir. Thierry Onkelinx
> > Instituut voor natuur- en bosonderzoek team Biometrie &
> Kwaliteitszorg
> > Gaverstraat 4 9500 Geraardsbergen Belgium
> >
> > Research Institute for Nature and Forest team Biometrics & Quality
> > Assurance Gaverstraat 4 9500 Geraardsbergen Belgium
> >
> > tel. + 32 54/436 185
> > Thierry.Onkelinx at inbo.be
> > www.inbo.be
> >
> > To call in the statistician after the experiment is done may be no
> > more than asking him to perform a post-mortem examination:
> he may be
> > able to say what the experiment died of.
> > ~ Sir Ronald Aylmer Fisher
> >
> > The plural of anecdote is not data.
> > ~ Roger Brinner
> >
> > The combination of some data and an aching desire for an
> answer does
> > not ensure that a reasonable answer can be extracted from a
> given body
> > of data.
> > ~ John Tukey
> >
> >
> >> -----Oorspronkelijk bericht-----
> >> Van: r-help-bounces at r-project.org
> >> [mailto:r-help-bounces at r-project.org] Namens Mikkel Meyer Andersen
> >> Verzonden: donderdag 2 september 2010 13:30
> >> Aan: r-help at r-project.org
> >> Onderwerp: [R] nlme formula from model specification
> >>
> >> Dear R-community,
> >>
> >> I'm analysing some noise using the nlme-package. I'm
> writing in order
> >> to get my usage of lme verified.
> >>
> >> In practise, a number of samples have been processed by a machine
> >> measuring the same signal at four different channels.
> >> I want to model the noise. I have taken the noise (the
> signal is from
> >> position 1 to 3500, and after that there is only noise).
> >>
> >> My data looks like this:
> >> channel.matrix:
> >> pos channel0 channel1 channel2 channel3 samplenumber
> >> 1 3501 8 3 12 1 1
> >> 2 3502 3 7 0 14 1
> >> 3 3503 9 1 13 3 1
> >> 4 3504 3 7 3 14 1
> >> 5 3505 6 5 4 5 1
> >> 6 3506 7 0 16 0 1 ...
> >> 495 3995 5 2 9 9 1
> >> 496 3996 2 4 6 10 1
> >> 497 3997 3 2 7 7 1
> >> 498 3998 2 4 3 9 1
> >> 499 3999 3 1 6 11 1
> >> 500 4000 0 3 6 7 1
> >> 2301 3501 1 4 3 9 2
> >> 2302 3502 3 3 4 13 2
> >> 2303 3503 4 1 8 5 2
> >> 2304 3504 3 1 10 2 2
> >> 2305 3505 2 3 5 8 2
> >> 2306 3506 0 5 8 2 2 ...
> >>
> >> The model is
> >> channel0 ~ alpha_i + eps_{i, j} + channel1 + channel2 +
> >> channel3 where i is sample number, j is position, and:
> >> alpha_i: fixed effect for each samplenumber
> >> eps_{i, j}: random effect, here with correlation
> >> structure as AR(1)
> >> channel1, ..., channel3: fixed effect for each channel not
> >> depending on
> >> samplenumber nor position
> >>
> >> (And then afterwards I would model channel1 ~ ... + channel2
> >> + channel3 etc.)
> >>
> >> I then use this function call:
> >> channel.matrix.grouped <- groupedData(channel0 ~ pos |
> samplenumber,
> >> data = channel.matrix)
> >>
> >> fit <- lme(channel0 ~ pos + samplenumber + channel1 +
> >> channel2 + channel3,
> >> random = ~ pos | samplenumber,
> >> correlation = corAR1(value = 0.5, form = ~ pos | samplenumber),
> >> data = channel.matrix.grouped)
> >>
> >> Is that the right way to express the model in (n)lme-notation?
> >>
> >> Cheers, Mikkel.
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide
> >> http://www.R-project.org/posting-guide.html
> >> and provide commented, minimal, self-contained, reproducible code.
> >>
> >
> > Druk dit bericht a.u.b. niet onnodig af.
> > Please do not print this message unnecessarily.
> >
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> > bericht niet bevestigd is door een geldig ondertekend document. The
> > views expressed in this message and any annex are purely
> those of the
> > writer and may not be regarded as stating an official position of
> > INBO, as long as the message is not confirmed by a duly
> signed document.
> >
>
Druk dit bericht a.u.b. niet onnodig af.
Please do not print this message unnecessarily.
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in this message
and any annex are purely those of the writer and may not be regarded as stating
an official position of INBO, as long as the message is not confirmed by a duly
signed document.
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